Version-1996.2 Release Notes

This release sees many bug fixes, but few truely new features. The most
noticable gap4 changes are the considerable speed improvements to gap4 and two
new assembly engines (forthcoming). In addition new features include a new text
based contig selector to supplement the existing graphical display, an
improved check assembly function and the removal of a few size limitations.

The new assembly engines are Xiaoqiu Huang's CAP2 and Gene Myer's FAKII
programs. For both of these we have the written the first versions of the gap4
interface. However we are not distributing either the Cap2 or FakII binaries
and hence the Gap4 options are currently "greyed out". Both assembly systems
have been modified to support Experiment Files. We hope to make a cap2 binary
available ourselves soon. The mechanism of obtaining FAKII will be to obtain
it direct from the authors, however our modified version is not yet available.
Announcements for both will appear on the
bionet.software.staden newsgroup
when we are ready.

The second new assembly engine is Gene Myer's FAKII program. Once again, the
Gap4 section is complete (first draft). We have made changes to the FAKII
source code to output Experiment File format. At some (unspecified) later date
the modified FAKII program will be available direct from Gene Myers.

For sip4 the most notable improvements, bug fixes excluded, are the ability to
display alignments in a graphical fashion, the ability to now use personal
sequence files of any length and to search them as libraries (entryname only),
and a new exact match search in the sequence browser.

The trial versions of the programs that examine traces to determine where to
clip readings based on their quality (trace_clip and scale_trace_clip) have
been substantially altered.

Finally, several new programs are available. These are:

copy_db

Copies and garbage collects gap4 databases.

extract_seq

Extracts the sequence component from trace files or
experiment files.

getABIstring

Displays arbitrary string fields from an ABI trace file.

getABIcomment

Displays the comments from an ABI trace file. Equivalent to
getABIstring CMNT.

Gap4 specific IO speedups gained by delaying data flushes, use of
data caching, and various other changes. Speedups vary from 17% faster
for assembly to over 900% for enter tags. Disk I/O should also be
reduced. See News: Gap4 Speed Improvments
for a detailed
summary.

Suggest Probes is now around 60% faster.

Contig Editor

Attempting to view an experiment file as a trace in gap4 no longer
crashes.

Possible memory corruption fixed in editor when resizing the editor to
a large (over double the original size) width.

Automatically quits the editor when we attempt to edit this contig by
another means and the editor has not yet been used to make changes.

Stop codons in the translation status lines are now shown in red.

Improved dialogue for 'join contigs'. It's now possible to easily
select both contigs using the contig selector by clicking on the
appropriate box in the join contigs dialogue.

Searching for tags that missed tags that overlap the cutoff data at
the left end when reveal cutoffs was not set.

The temporary tags created on the consensus by the Select Primer
routine caused in-memory tag list confusion. Either the editor would
crash later in routines such as align, or another consensus tag would
be completely lost.

Join highlighting of reading names/lines between the editor and the
template displays was causing harmless warnings when highlighting the
consensus line.

Fixed odd font issue under Solaris.

Undoing cutoff adjustments in the join editor now maintains lock
position properly.

Misc

Joins made during assembly would sometimes corrupt the contig order.
Now fixed. (NB: to recover from contig order corruptions simply select
"Reset contig order" from the commands menu of Doctor
Database.

Fixed bug with the editor cursor as displayed in the template display.
It had problems with negative cursor positions and didn't always draw
itself until the editor was used to move the cursor.

We can now double middle click on the template display (including the
quality plot) to bring up a contig editor at a specific point or to
move the existing editor to the new point.

The oligo selection dialogue in both the manual (editor) and automatic
modes has extra parameters available.

Removed the limitation of 100,000 records per database (also fixed for
gap/xgap).

Removed tags and disassembled readings are now reclaimed in the
database properly for subsequent usage.

Default unix permissions for gap databases are now to write with
whatever the user's umask value requests. Previously we blocked
read-write access for group and others even when umask stated
otherwise.

Fixed 'database open' detection code. It crashed when we closed a
database by using 'new' (and cancel it) followed by 'open'. We also
now close any current database before using the file browser (was
after) to fix busy file confusion.

Fixed an uninitialised variable in "assemble all readings in one
contig" which caused the routine to get stuck on SGI machines

Check assembly now uses a window to slide along the used data when
checking for mismatch percentages. This means that long, good
matching, readings with diverging sequences at one end are easily
detectable.

Disassemble readings and directed assembly both crashed when the
database after the actions is blank (either removed all, or assembled
none). Fixed.

The output window can now display the parameters used to produce
certain types of output (right button).

Uninitialised variable caused rare case where the confidence values
were not read from SCF files during assembly.

The Suggest Probes function now has a user interface to select which
oligos to write to a file and tags to create.

Alignment output when joining two contigs now displays the percentage
mismatch instead of a score.

Automatic scaling of the stop codon and restriction enzyme plots now
occurs when specifying the ranges in the contig to display.

Contigs outputted by calculate consensus (and other functions) are now
generated in the order shown in the contig selector.

Added a new form of contig selector that allows selection from a
textual list rather than the existing graphical plot.

Enter Preassembled data was incorrectly using the vector information
for determining 'good' regions of sequence. In rare cases these may be
different from the QL/QR lines and hence used to cause misalignments
after assembly.

Removed the limitation on the maximum size of tags (was 1024 letters).

Force dumping of core when receiving a fatal database error. This is
deliberate to aid debugging.

Assembly now handles the distinction between filenames and reading
names correctly. Previously, when checking if a reading was already
entered, it used the filename to compare against the list of currently
entered readings

Assembly into one contig now works on non-blank databases.

Suggest Probes on extremely short contigs used to produce incorrect
results.

Now blocks against attempting to edit sequences when the edits line is

not displayed.
The default edit mode is now 'right cutoff'.

Attempting to edit the sequence or position the cursor when no trace
has been loaded no longer causes errors.

Sped up redrawing the cursor in the trace display. This speeds up
the gap4 display too.

Added -editscf command line option to allow writing of the SCF format.
Disabled by default as it can be dangerous without appropriate
knowledge.

Fixed help.

Io_lib

The extract_seq program is now distributed as a binary (we only
supplied source before). It now also accepts parameters for clipping
good quality data from experiment files.

The experiment file output of io_lib (used by trev and gap4 'extract
readings' amongst other things) could write tags incorrectly. The code
now also knows which line types should be written only once and which
could be written many times.

Writing to plain sequence format (io_lib) no longer produces an error
message. It worked before, but claimed otherwise.

Added back code to update the private data in the SCF file format.
This was 'lost' sometime after io_lib v1.2.

Removed a small memory leak in 'deallocating' SCF structures.

Experiment file output sometimes produced too much output for ON and
AV lines when they ended exactly on a new line boundary. This affected
the Gap4 extract readings command.

Better error recovery where the comments in an SCF file are missing.
This used to crash.

Misc

Can now search for text in the output window for both gap4 and sip4.

The time output format of the output windows (gap4 and sip4) is now
more similar to the Unix 'date' command - it contains week days as
well as day of month.

The 'scale' controls in gap4, sip4, etc, now take up less room on the
screen. They also handle key bindings better. This means that the
larger dialogues, such as Gap4's Find Internal Joins have now shrunk
and should fit better on small screens.

New copy database (copy_db) program. This allows copying of single
databases with some database garbage collection, and also allow simple
cases of merging databases.

Large revamp of the source building mechanism (Makefiles). General
tidy up of code too.

Alfsplit now only uses the name field in the ALF files when it
contains printable characters with no white space or slash characters.
Otherwise the filename is used as the reading name.

Version-1996.2.1 Update

This consists of a minor update to 1996.2 containing a few bug fixes:

Shuffle pads had a memory overflow that could occasionally corrupt
the data within the editor. This does not directly corrupt the database
permanently, but will do so if the data in the editor is then saved.

Tags added to experiments files prior to assembly could be placed
in the wrong location (by a few bases, depending on the number of pads
to the reading). This only affects the normal shotgun assembly mode.

The default font for the tk dialogue boxes does not exist on
Solaris systems without the optional SUNWxwoft package installed.
Changing the font from -Adobe-Times-... to -*-Times-... has hopefully
fixed the problem.